On Nov 14, 2011, the article "DNA-encoded chemical libraries: 20 years of revolutionizing drug discovery" provides a comprehensive review of the evolution and impact of DNA-encoded library (DEL) technology over the past two decades. Originally conceptualized in 1992 by Brenner and Lerner, DELs have matured from a theoretical framework into a powerful platform that integrates synthetic chemistry with molecular biology, enabling efficient ligand discovery for diverse protein targets. The review systematically covers the foundational principles, design strategies, screening advancements, and practical applications of DELs, highlighting their transformation from academic concepts to widely adopted tools in drug development.

The Foundation of DNA-Encoding Technology

DEL technology operates on a simple yet powerful principle: each chemical compound in a library is covalently linked to a unique DNA tag that serves as an amplifiable identification barcode. This ingenious system creates a physical connection between the "phenotype" (the small molecule) and its "genotype" (the DNA sequence), mirroring established display technologies like antibody phage display but extending the concept to synthetic organic compounds.

Fig. 1. Conceptual analogy between display technologies and DELs. (Mannocci, et al., 2011)

The methodology allows for affinity-based selection of ligands at sub-picomolar concentrations, with the DNA tag enabling amplification and identification of binding compounds through high-throughput sequencing. This approach eliminates many limitations of conventional high-throughput screening (HTS), which requires individual testing of hundreds of thousands of compounds and substantial resources.

Library Design and Construction Strategies

DEL technology has evolved along two primary design philosophies: single-pharmacophore libraries and dual-pharmacophore libraries. Single-pharmacophore libraries display individual organic molecules on DNA tags and can be constructed using either split-and-pool combinatorial synthesis or DNA-templated strategies.

Fig. 2. The pioneering concept of a DNA-encoded chemical library. (Mannocci, et al., 2011)

The split-and-pool approach, developed by several research groups including those at GlaxoSmithKline and ETH Zurich, involves sequential coupling of building blocks to DNA tags with encoding steps interspersed between chemical reactions. This method has enabled the creation of libraries containing millions to billions of compounds.

Fig.3 Two principal architectures of DELs. (Mannocci, et al., 2011)

Dual-pharmacophore libraries, exemplified by the encoded self-assembling chemical (ESAC) libraries pioneered by ETH Zurich researchers, employ a different strategy. These libraries consist of two sub-libraries that hybridize combinatorially, displaying pairs of chemical entities at opposite ends of DNA heteroduplexes. This approach benefits from the chelate effect, where simultaneous binding of two adjacent molecules to different sites on a target protein can significantly enhance affinity.

Advancements in Screening and Data Analysis

The true power of DEL technology emerged with the development of next-generation sequencing platforms. Modern sequencing technologies allow researchers to simultaneously analyze millions of DNA tags, providing unprecedented insights into library composition and selection outcomes.

Fig.4 Statistical analysis of DEL sequencing data before and after selection. (Mannocci, et al., 2011)

Statistical analysis of sequencing data enables researchers to distinguish genuine binders from background noise by comparing tag frequencies before and after selection. This quantitative approach has made DEL technology particularly valuable for tackling challenging targets, including proteins involved in protein-protein interactions that have historically been difficult to drug.

Practical Applications and Success Stories

The proof of concept for DEL technology has been demonstrated across multiple target classes. Early successes included isolations of binders against streptavidin, trypsin, carbonic anhydrase, and various kinases. More impressively, researchers have identified inhibitors against clinically relevant targets such as Bcl-xL (involved in apoptosis regulation) and TNF (a key inflammatory cytokine), with affinities reaching nanomolar ranges.

Library sizes have grown exponentially, from initial proof-of-concept libraries containing dozens of compounds to contemporary libraries comprising hundreds of millions of members. The technology has proven particularly valuable for affinity maturation campaigns, where initial lead structures are optimized through systematic variation of chemical substituents.

Modern Implementation at CD BioGlyco

Today, the principles outlined in this seminal review are implemented in cutting-edge research facilities like CD BioGlyco, which specializes in DNA-encoded Glycan Library (DEGL) technology. Building on the foundation established by early DEL pioneers, we offer comprehensive services including DEGL Design and optimization, DNA-compatible Reaction Development, Library Construction, High-throughput Screening, and sophisticated Data Analysis.

The company's expertise in glycan chemistry, combined with advanced DEL methodologies, enables researchers to explore carbohydrate-protein interactions with unprecedented efficiency. Our platforms support various library formats, including Single-pharmacophore, Dual-pharmacophore, and Multivalent DEGLs, tailored to specific research needs.

Future Perspectives

As DEL technology continues to evolve, several challenges remain. Library design must balance size with drug-like properties, as extremely large libraries often contain compounds with suboptimal physicochemical characteristics. Additionally, the field continues to develop more efficient encoding strategies and screening methodologies.

The integration of DEL technology with other emerging approaches, such as machine learning and structural biology, promises to further accelerate drug discovery. As sequencing technologies advance and library design principles refine, DEL platforms will likely become increasingly accessible to academic researchers and smaller biotech companies.

In conclusion, DNA-encoded chemical library technology has matured from a theoretical concept to a practical drug discovery tool with demonstrated success across multiple target classes. The pioneering work summarized in this 20-year retrospective continues to inspire innovation in combinatorial chemistry and ligand discovery, with companies like CD BioGlyco translating these principles into practical solutions for modern drug discovery challenges.